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  <title>2 Global search genes by IDs, functions, and pathways | IMP: Bridging the Gap for Medicinal Plant Genomics</title>
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<meta name="author" content="Chen Tong" />
<meta name="author" content="Address: https://www.bic.ac.cn/IMP" />
<meta name="author" content="chent@nrc.ac.cn / chentong_biology@163.com" />


<meta name="date" content="2023-06-30" />

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<li><a href="index.html#overview-of-imp" id="toc-overview-of-imp">Overview of IMP</a></li>
<li><a href="geneannotation.html#geneannotation" id="toc-geneannotation"><span class="toc-section-number">1</span> Systematic prediction and annotation of included genomes</a>
<ul>
<li><a href="geneannotation.html#genomeumltipleassembl" id="toc-genomeumltipleassembl"><span class="toc-section-number">1.1</span> Species with multiple genome assembles</a></li>
<li><a href="geneannotation.html#genome_without_assembl" id="toc-genome_without_assembl"><span class="toc-section-number">1.2</span> Species without published genome assembles</a></li>
</ul></li>
<li><a href="global-search.html#global_search" id="toc-global_search"><span class="toc-section-number">2</span> Global search genes by IDs, functions, and pathways</a>
<ul>
<li><a href="global-search.html#gene_detail_page" id="toc-gene_detail_page"><span class="toc-section-number">2.1</span> Gene detail page</a></li>
<li><a href="global-search.html#the-send-to-buttons" id="toc-the-send-to-buttons"><span class="toc-section-number">2.2</span> The send to buttons</a></li>
</ul></li>
<li><a href="browse-species-genes.html#browse_species_genes" id="toc-browse_species_genes"><span class="toc-section-number">3</span> Browse species and genes</a>
<ul>
<li><a href="browse-species-genes.html#structure-of-the-browse-page" id="toc-structure-of-the-browse-page"><span class="toc-section-number">3.1</span> Structure of the Browse page</a></li>
<li><a href="browse-species-genes.html#structure-of-the-species-detail-page" id="toc-structure-of-the-species-detail-page"><span class="toc-section-number">3.2</span> Structure of the species detail page</a></li>
</ul></li>
<li><a href="degeneanalysis.html#degeneanalysis" id="toc-degeneanalysis"><span class="toc-section-number">4</span> DE Gene analysis</a>
<ul>
<li><a href="degeneanalysis.html#overviewStructureform" id="toc-overviewStructureform"><span class="toc-section-number">4.1</span> Overview the structure of module page</a></li>
<li><a href="degeneanalysis.html#firststepoptionsrequiredpara" id="toc-firststepoptionsrequiredpara"><span class="toc-section-number">4.2</span> First step: choose options for each required parameter</a></li>
<li><a href="degeneanalysis.html#secondstepsamplecorre" id="toc-secondstepsamplecorre"><span class="toc-section-number">4.3</span> Second step: check sample correlation profile and filter outlier samples</a>
<ul>
<li><a href="degeneanalysis.html#outliersampleasm" id="toc-outliersampleasm"><span class="toc-section-number">4.3.1</span> Automatical or manual detection of outlier samples</a></li>
<li><a href="degeneanalysis.html#interactiveheatmappca" id="toc-interactiveheatmappca"><span class="toc-section-number">4.3.2</span> Interactive heatmap showing sample correlation profiles</a></li>
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<li><a href="degeneanalysis.html#thirdstep" id="toc-thirdstep"><span class="toc-section-number">4.4</span> Third step: Set compare groups</a></li>
<li><a href="degeneanalysis.html#forthstep" id="toc-forthstep"><span class="toc-section-number">4.5</span> Forth step: Set filtering thresholds for DE genes screening</a></li>
<li><a href="degeneanalysis.html#fifthstep" id="toc-fifthstep"><span class="toc-section-number">4.6</span> Fifth step: an overview of samples information and analysis parameter information</a></li>
<li><a href="degeneanalysis.html#degeneanalysisresultsreport" id="toc-degeneanalysisresultsreport"><span class="toc-section-number">4.7</span> Sixth step: DE Gene analysis results report</a></li>
<li><a href="degeneanalysis.html#exportpdf" id="toc-exportpdf"><span class="toc-section-number">4.8</span> Export to PDF</a></li>
</ul></li>
<li><a href="geneexpressionprofile.html#geneexpressionprofile" id="toc-geneexpressionprofile"><span class="toc-section-number">5</span> Gene expression profile</a>
<ul>
<li><a href="geneexpressionprofile.html#overviewStructureform2" id="toc-overviewStructureform2"><span class="toc-section-number">5.1</span> Overview the structure of module page</a></li>
<li><a href="geneexpressionprofile.html#coferp13" id="toc-coferp13"><span class="toc-section-number">5.2</span> Choose options for each required parameters step by step</a></li>
<li><a href="geneexpressionprofile.html#gepdemo" id="toc-gepdemo"><span class="toc-section-number">5.3</span> The demo button</a></li>
<li><a href="geneexpressionprofile.html#precisefuzzy" id="toc-precisefuzzy"><span class="toc-section-number">5.4</span> The precise search and fuzy search mode</a></li>
</ul></li>
<li><a href="GOKEGGenrichmentanalysis.html#GOKEGGenrichmentanalysis" id="toc-GOKEGGenrichmentanalysis"><span class="toc-section-number">6</span> GO/KEGG enrichment analysis</a>
<ul>
<li><a href="GOKEGGenrichmentanalysis.html#pgkea5" id="toc-pgkea5"><span class="toc-section-number">6.1</span> Principles of over-representation enrichment analysis</a></li>
<li><a href="GOKEGGenrichmentanalysis.html#coferp32" id="toc-coferp32"><span class="toc-section-number">6.2</span> Choose options for each required parameters step by step</a></li>
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<li><a href="genefishing.html#genefishing" id="toc-genefishing"><span class="toc-section-number">7</span> Gene fishing</a>
<ul>
<li><a href="genefishing.html#genefishingcoferp5" id="toc-genefishingcoferp5"><span class="toc-section-number">7.1</span> Choose options for each required parameters step by step</a></li>
<li><a href="genefishing.html#networktoolkit" id="toc-networktoolkit"><span class="toc-section-number">7.2</span> Network toolkit</a></li>
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<li><a href="GSEAenrichmentanalysis.html#GSEAenrichmentanalysis" id="toc-GSEAenrichmentanalysis"><span class="toc-section-number">8</span> GSEA enrichment analysis</a>
<ul>
<li><a href="GSEAenrichmentanalysis.html#pgsea5" id="toc-pgsea5"><span class="toc-section-number">8.1</span> Principles of gene set enrichment analysis (GSEA)</a></li>
<li><a href="GSEAenrichmentanalysis.html#coferp22" id="toc-coferp22"><span class="toc-section-number">8.2</span> Choose options for each required parameters step by step</a></li>
<li><a href="GSEAenrichmentanalysis.html#gsearef" id="toc-gsearef"><span class="toc-section-number">8.3</span> References</a></li>
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<li><a href="genemapviewer.html#genemapviewer" id="toc-genemapviewer"><span class="toc-section-number">9</span> Gene map viewer</a>
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<li><a href="genemapviewer.html#coferp5" id="toc-coferp5"><span class="toc-section-number">9.1</span> Choose options for each required parameters step by step</a></li>
<li><a href="genemapviewer.html#oam31" id="toc-oam31"><span class="toc-section-number">9.2</span> Overlay and annotation mode</a></li>
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<li><a href="blast.html#blast" id="toc-blast"><span class="toc-section-number">10</span> BLAST - Basic Local Alignment Search Tool</a>
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<li><a href="blast.html#cusmBLAST5" id="toc-cusmBLAST5"><span class="toc-section-number">10.1</span> Customizable BLAST</a></li>
<li><a href="blast.html#blasthtmlresult" id="toc-blasthtmlresult"><span class="toc-section-number">10.2</span> BLAST HTML results</a></li>
<li><a href="blast.html#blasttableresult" id="toc-blasttableresult"><span class="toc-section-number">10.3</span> BLAST Table results</a></li>
<li><a href="blast.html#refblast" id="toc-refblast"><span class="toc-section-number">10.4</span> Reference</a></li>
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<li><a href="msa.html#msa" id="toc-msa"><span class="toc-section-number">11</span> Multiple sequence alignment</a>
<ul>
<li><a href="msa.html#sbmsa05" id="toc-sbmsa05"><span class="toc-section-number">11.1</span> Sequences based multiple sequence alignment</a></li>
<li><a href="msa.html#gtidbmsa27" id="toc-gtidbmsa27"><span class="toc-section-number">11.2</span> Gene/Transcript IDs based multiple sequence alignment</a></li>
<li><a href="msa.html#refmafft" id="toc-refmafft"><span class="toc-section-number">11.3</span> Reference</a></li>
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<li><a href="sequencefetch.html#sequencefetch" id="toc-sequencefetch"><span class="toc-section-number">12</span> Sequences fetch</a></li>
<li><a href="primerdesign.html#primerdesign" id="toc-primerdesign"><span class="toc-section-number">13</span> Primer design</a>
<ul>
<li><a href="primerdesign.html#primerdesigngeneids" id="toc-primerdesigngeneids"><span class="toc-section-number">13.1</span> Primer design for genes with IDs as input</a></li>
</ul></li>
<li><a href="igvbrowser.html#igvbrowser" id="toc-igvbrowser"><span class="toc-section-number">14</span> IGV browser</a>
<ul>
<li><a href="igvbrowser.html#vepigv" id="toc-vepigv"><span class="toc-section-number">14.1</span> Visualizing expression profiles</a></li>
</ul></li>
<li><a href="download.html#download" id="toc-download"><span class="toc-section-number">15</span> Download</a></li>
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          <h1>
            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">IMP: Bridging the Gap for Medicinal Plant Genomics</a>
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<div id="global_search" class="section level1" number="2">
<h1><span class="header-section-number">2</span> Global search genes by IDs, functions, and pathways</h1>
<p>On the index page, a global search function is provided for quickly accessing one or a series of genes. Normally, we may not remember the IDs of genes. But, we could search genes by function descriptions or keywords. This would facilitate the usage of IMP.</p>

<div class="figure" style="text-align: center"><span id="fig:unnamed-chunk-4"></span>
<img src="image/index_1.png" alt="A screenshot of the index page." width="100%" />
<p class="caption">
Figure 2.1: A screenshot of the index page.
</p>
</div>
<p>For example, we want to search for <code>cytochrome p450</code> genes in <code>Andrographis paniculata</code>. We could operate in the following 3 steps:</p>

<div class="figure" style="text-align: center"><span id="fig:unnamed-chunk-5"></span>
<img src="image/index_global_search_andro.png" alt="Searching for cytochrome p450 genes in Andrographis paniculata using the global search function." width="100%" />
<p class="caption">
Figure 2.2: Searching for <code>cytochrome p450</code> genes in <code>Andrographis paniculata</code> using the global search function.
</p>
</div>
<p>Totally, 501 related genes are returned. From the descriptions, we could see some genes are Cytochrome P450 (these are what we searched).</p>
<p><img src="image/index_global_search_andro_result.png" width="100%" style="display: block; margin: auto;" /></p>
<p>Some genes are glutathione s-transferase and UDP-Glycosyltransferase. This is not wrong since the keyword <code>Cytochrome P450</code> must be contained in one of their functional annotations. We could check the detailed information of these genes by clicking the gene names.</p>
<div id="gene_detail_page" class="section level2" number="2.1">
<h2><span class="header-section-number">2.1</span> Gene detail page</h2>
<p>As for transcript <code>IMPTApa2N34540_1</code>, this is a <code>Flavin-binding monooxygenase-like</code> gene. The below screenshot could be classified into 5 parts.</p>
<ol style="list-style-type: decimal">
<li><p>The basic annotation information like <code>Gene locus</code>, <code>Transcript locus</code>, <code>Preferred name</code>, <code>Gene description</code>, <code>GO term name</code>, <code>KEGG Pathway</code>, <code>KEGG KO Name</code>, <code>COG category</code>. One could click the blue text to tour Gene ontology, and the KEGG database for more information. Normally, these page transitions are not required.</p></li>
<li><p>The sequence part contains <code>Gene</code>, <code>CDS</code>, <code>Promoter</code> (upstream 2 kilobases of the transcription start site as defined as promoters here), and <code>Protein</code> sequences of the gene. These sequences could be directly copied or downloaded for other usages.</p></li>
<li><p>Expression profile part showing the expression status of this gene in given datasets. One could change to <code>Log2</code> transformed expression value, or change the layout or sorting ways.</p></li>
</ol>
<blockquote>
<p>Note</p>
<p>Especially, if X-axis tick names are very long, one could modify the padding options to show whole names.</p>
</blockquote>
<blockquote>
<p>Note</p>
<p>Click the legend in the interactive plot could show or hide specified parts.</p>
</blockquote>
<ol start="4" style="list-style-type: decimal">
<li><p>Gene structure part showing the <code>UTRs</code>, <code>Start/Stop codons</code>, and <code>CDS</code> of this gene.</p></li>
<li><p>Protein functional domain part showing the predicted PFAM domains of proteins encoded by this transcript. One could click the domain block to tour to EBI Pfam domain page to check the detailed information on these domains.</p></li>
</ol>
<blockquote>
<p>Note</p>
<p>Pictures with a <code>Save SVG</code> button could be saved in vector format. If one wants the result in PNG format, a screenshot would generate high-quality results.</p>
</blockquote>
<p><img src="image/gene_detail_IMPTApa2N34540_1.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="the-send-to-buttons" class="section level2" number="2.2">
<h2><span class="header-section-number">2.2</span> The send to buttons</h2>
<p>Below the result table, there are several buttons that could help to transfer selected genes to specialized modules for further exploration.</p>
<p>This is feasible and could spare the typing of gene names one by one. The description of these modules would be listed on each module help page.</p>
<p><img src="image/send_to_buttons_search_detail.png" width="100%" style="display: block; margin: auto;" /></p>

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